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Yorodumi- PDB-4d9m: Crystal structure of Diaminopropionate ammonia lyase from Escheri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d9m | ||||||
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Title | Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with aminoacrylate-PLP azomethine reaction intermediate | ||||||
Components | Diaminopropionate ammonia-lyase | ||||||
Keywords | LYASE / Fold type II PLP-dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily | ||||||
Function / homology | Function and homology information diaminopropionate ammonia-lyase / diaminopropionate ammonia-lyase activity / pyridoxal phosphate binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bisht, S. / Rajaram, V. / Bharath, S.R. / Murthy, M.R.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis Authors: Bisht, S. / Rajaram, V. / Bharath, S.R. / Kalyani, J.N. / Khan, F. / Rao, A.N. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d9m.cif.gz | 288.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d9m.ent.gz | 237.7 KB | Display | PDB format |
PDBx/mmJSON format | 4d9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d9m_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4d9m_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4d9m_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 4d9m_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/4d9m ftp://data.pdbj.org/pub/pdb/validation_reports/d9/4d9m | HTTPS FTP |
-Related structure data
Related structure data | 4d9gC 4d9iSC 4d9kC 4d9nC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43372.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2871, JW2839, ygeX / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P66899, diaminopropionate ammonia-lyase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 40mM tris HCl pH 8.3, Crystals were soaked with 10mM DL-2,3-Diaminopropanoate in crystallization condition ...Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 40mM tris HCl pH 8.3, Crystals were soaked with 10mM DL-2,3-Diaminopropanoate in crystallization condition for 10 hrs before data collection., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 13, 2010 / Details: Mirror |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 26585 / % possible obs: 97.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1291 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D9I Resolution: 2.5→45.29 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.878 / SU B: 22.555 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.884 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.544 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.498→2.563 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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